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Page 14 of 20 Linehan et al. Microbiome Res Rep. 2025;4:24 https://dx.doi.org/10.20517/mrr.2024.92

C. pyruviciproducens, present in all dyads, was the only shared species between oral and vaginal samples. It
[79]
is a pyruvic acid producer and potential pathogen . F. nucleatum was also highly prevalent, present in 15
dyads. For maternal oral transfer to meconium, an average of eight bacterial taxa (6% of reads) were shared,
with R. mucilaginosa being the only universally shared species, known for its anti-inflammatory
properties . Vaginal-to-meconium sharing included 38 taxa, accounting for 21% of reads, with B. longum
[80]
found in all dyads. B. longum is a key commensal of the gut microbiota, with beneficial effects on neonatal
health [81-83] .

The final aim of this study was to explore factors that influence microbial strain inheritance and/or selection
in infants. These factors provide insight into the development of early-life medical conditions and could
inform new preventive treatments. Maternal antibiotic use had a significant impact on the beta diversity of
meconium. Opportunistic pathogens like Gemella and Fusobacterium spp. were differentially abundant in
infants of mothers who received antibiotics, with an increase in heme biosynthesis pathways, critical for

bacterial virulence [84,85] . Similar results were found in maternal saliva, where Prevotella and Fusobacterium
spp., linked to periodontitis, were abundant in antibiotic-exposed groups . Vaginal microbiome diversity
[86]
also increased with antibiotic use, reducing Lactobacillus spp., known for maintaining vaginal health .
[87]
Functional pathways, including those related to succinate production, which supports bacterial vaginosis,
were enriched in the antibiotic group [88-90] . Delivery mode affected meconium diversity, with Intestinibacter
and Veillonella spp. prominent in CS infants . NB infants displayed more commensal bacteria like
[91]
[92]
Bifidobacterium, linked to lactic acid production and gut health . In the infant oral microbiome, delivery
mode shaped the prevalence of Bifidobacterium longum and Veillonella parvula in NB infants, whereas
L. mirabilis, associated with periodontal health, was enriched in CS infants [93,94] . CS delivery also affected
maternal oral microbiota, enriching Fusobacterium spp., associated with periodontitis, while NB mothers
had higher levels of Streptococcus oralis and Actinomyces [95,96] . Feeding type played a key role in microbial
colonization, with breastfed infants enriched in Bacteroides spp., capable of metabolizing human milk
oligosaccharides (HMOs) [97,98] . Formula-fed infants had a more diverse microbiota, including Blautia spp.
and Dorea spp., typically seen in more mature gut microbiomes . Breastfeeding was linked to health-
[99]
promoting metabolic pathways, including vitamin K2 and vitamin B6 biosynthesis, essential for immune
[100]
function and metabolism . Gender differences were limited, with no significant functional shifts in the
meconium microbiome, though certain taxa, such as B. animalis and B. uniformis, were more abundant in
females . These gender-specific differences remain poorly understood but are likely influenced by
[101]
[102]
hormonal and immune interactions . PROM impacted meconium, maternal oral, and vaginal
microbiomes. PROM increased alpha diversity in the vaginal microbiome and reduced Lactobacillus spp., a
[103]
critical protector of vaginal health . In maternal oral samples, the pathogen Capnocytophaga leadbetteri
was enriched, but PROM was also associated with pathogen-clearing pathways, such as nitrate
[104]
reduction . These results align with studies suggesting a lack of Lactobacillus spp. is linked to PROM
[105]
occurrence, and clinical trials have explored probiotic treatments for PROM .
There are several limitations to this study. Firstly, the use of a small subset of samples may have limited the
ability to draw precise and broadly applicable conclusions regarding the impact of perinatal factors on the
infant microbiome. A larger sample size would provide greater statistical power and more robust analyses.
Additionally, the cross-sectional design prevents tracking microbiome changes over time, highlighting the
need for longitudinal studies to understand its development and environmental influences. The limitations
of 16S rRNA gene sequencing also restrict the ability to reach definitive conclusions, as it provides lower
taxonomic resolution than shotgun sequencing, often limiting identification to the genus level. This hinders
differentiation between pathogenic and non-pathogenic strains within genera, making it challenging to infer
vertical transmission with certainty. However, genus-level identification may still provide valuable insights,